Variant report

Variant	rs349045
Chromosome Location	chr19:44299892-44299893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10401170	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10401203	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10426528	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11665924	0.83[CHB][hapmap]
rs349046	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs349047	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs349048	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs349049	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs349050	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs349053	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs349055	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3760982	0.83[CHB][hapmap]
rs3760983	0.83[CHB][hapmap]
rs56103707	0.86[ASN][1000 genomes]
rs62116990	0.90[ASN][1000 genomes]
rs62116991	0.86[ASN][1000 genomes]
rs8104447	0.93[ASN][1000 genomes]
rs8111664	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Reading or mathematical ability	25003214	GWAS catalog

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs349045	ZNF404	cis	multi-tissue	Pritchard
rs349045	LYPD5	trans	brain	seeQTL
rs349045	FLJ30469	cis	multi-tissue	Pritchard
rs349045	ZNF404	trans	parietal	SCAN
rs349045	LYPD5	cis	brain	seeQTL
rs349045	KDELR1	cis	parietal	SCAN
rs349045	LRRC4B	cis	parietal	SCAN
rs349045	AC115522.3	cis	Skin Sun Exposed Lower leg	GTEx
rs349045	KCNN4	cis	Whole Blood	GTEx
rs349045	CD3EAP	cis	cerebellum	SCAN
rs349045	ZNF296	cis	parietal	SCAN
rs349045	ZNF296	cis	cerebellum	SCAN
rs349045	GEMIN7	cis	cerebellum	SCAN
rs349045	KCNN4	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44289400-44302600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44289800-44300800	Weak transcription	Placenta	Placenta
3	chr19:44290000-44302400	Weak transcription	NHEK	skin
4	chr19:44290200-44302200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:44298400-44300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:44299000-44302000	Weak transcription	Brain Angular Gyrus	brain
7	chr19:44299600-44301400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:44299600-44302200	Weak transcription	Brain Anterior Caudate	brain
9	chr19:44299600-44302400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:44299800-44300000	ZNF genes & repeats	Adipose Nuclei	Adipose

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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